Mixing and Mating of Modern Humans with Other Hominins

Home | Category: First Modern Humans (400,000-20,000 Years Ago)

Maddie Burakoff and Laura Ungar of Associated Press wrote: What does it mean to be human? For a long time, the answer seemed clear. Our species, Homo sapiens — with our complex thoughts and deep emotions — were the only true humans to ever walk the Earth. Earlier forms, like the Neanderthals, were thought to be just steps along the path of evolution, who died out because we were better versions. [Source: Maddie Burakoff and Laura Ungar, Associated Press, September 24, 2023]

That picture is now changing. In recent years, researchers have gained the power to pull DNA from ancient hominins, including our early ancestors and other relatives who walked on two legs. Ancient DNA technology has revolutionized the way we study human history and has quickly taken off, with a constant stream of studies exploring the genes of long-ago people.

Along with more fossils and artifacts, the DNA findings are pointing us to a challenging idea: We're not so special. For most of human history we shared the planet with other kinds of early humans, and those now-extinct groups were a lot like us. “We can see them as being fully human. But, interestingly, a different kind of human,” said Chris Stringer, a human evolution expert at London’s Natural History Museum. “A different way to be human.” What's more, humans had close — even intimate — interactions with some of these other groups, including Neanderthals, Denisovans and “ghost populations” we only know from DNA. “It’s a unique time in human history when there are only one of us,” Stringer said.

Human evolution was not about “survival of the fittest and extinction,” said John Hawks, a paleoanthropologist at the University of Wisconsin-Madison. It’s about “interaction and mixture.”

Scientists can’t get useful genetic information out of every fossil they find, especially if it’s really old or in the wrong climate. They haven't been able to gather much ancient DNA from Africa, where Homo sapiens first evolved, because it has been degraded by heat and moisture. Still, many are hopeful that as DNA technology keeps advancing, we’ll be able to push further into the past and get ancient genomes from more parts of the world, adding more brushstrokes to our picture of human history. Because even though we were the only ones to survive, the other extinct groups played a key role in our history, and our present. They are part of a common humanity connecting every person, said Mary Prendergast, a Rice University archeologist. “If you look at the fossil record, the archeological record, the genetic record," she said, "you see that we share far more in common than what divides us.”

Only Seven Percent of Our DNA Is Unique to Modern Humans

Just 7 percent of our genome is uniquely shared with other humans, and not shared by other early ancestors, according to a study published in July 2021 in the journal Science Advances. “That's a pretty small percentage," said Nathan Schaefer, a University of California computational biologist and co-author of the new paper. “This kind of finding is why scientists are turning away from thinking that we humans are so vastly different from Neanderthals.” [Source: Christina Larson, Associated Press, July 17, 2021]

Christina Larson of Associated Press wrote: “The research draws upon DNA extracted from fossil remains of now-extinct Neanderthals and Denisovans dating back to around 40,000 or 50,000 years ago, as well as from 279 modern people from around the world. Scientists already know that modern people share some DNA with Neanderthals, but different people share different parts of the genome. One goal of the new research was to identify the genes that are exclusive to modern humans. “It's a difficult statistical problem, and the researchers “developed a valuable tool that takes account of missing data in the ancient genomes,” said John Hawks, a paleoanthropologist at the University of Wisconsin, Madison, who was not involved in the research.

“The researchers also found that an even smaller fraction of our genome — just 1.5 percent — is both unique to our species and shared among all people alive today. Those slivers of DNA may hold the most significant clues as to what truly distinguishes modern human beings. “We can tell those regions of the genome are highly enriched for genes that have to do with neural development and brain function,” said University of California, Santa Cruz computational biologist Richard Green, a co-author of the paper.

“In 2010, Green helped produce the first draft sequence of a Neanderthal genome. Four years later, geneticist Joshua Akey co-authored a paper showing that modern humans carry some remnants of Neanderthal DNA. Since then, scientists have continued to refine techniques to extract and analyze genetic material from fossils. “Better tools allow us to ask increasingly more detailed questions about human history and evolution,” said Akey, who is now at Princeton and was not involved in the new research. He praised the methodology of the new study.

“However, Alan Templeton, a population geneticist at Washington University in St Louis, questioned the authors' assumption that changes in the human genome are randomly distributed, rather than clustered around certain hotspots within the genome. “The findings underscore "that we’re actually a very young species,” said Akey. “Not that long ago, we shared the planet with other human lineages.”

Many Hominins Lived at the Same Times as Modern Humans

Maddie Burakoff and Laura Ungar of Associated Press wrote: Scientists now know that after Homo sapiens first showed up in Africa around 300,000 years ago, they overlapped with a whole cast of other hominins, explained Rick Potts, director of the Smithsonian’s Human Origins Program. Neanderthals were hanging out in Europe. Homo heidelbergensis and Homo naledi were living in Africa. The short-statured Homo floresiensis, sometimes known as the “Hobbit,” was living in Indonesia, while the long-legged Homo erectus was loping around Asia. [Source: Maddie Burakoff and Laura Ungar, Associated Press, September 24, 2023]

Scientists started to realize all these hominins weren’t our direct ancestors. Instead, they were more like our cousins: lineages that split off from a common source and headed in different directions. Archaeological finds have shown some of them had complex behaviors. Neanderthals painted cave walls, Homo heidelbergensis hunted large animals like rhinos and hippos, and some scientists think even the small-brained Homo naledi was burying its dead in South African cave systems. A study last week found early humans were building structures with wood before Homo sapiens evolved.

Researcher also wondered: If these other kinds of humans were not so different, did our ancestors have sex with them? For some, the mixing was hard to imagine. Many argued that as Homo sapiens ventured out of Africa, they replaced other groups without mating. Archaeologist John Shea of New York’s Stony Brook University said he used to think of Neanderthals and Homo sapiens as rivals, believing “if they bumped into each other, they’d probably kill each other.”

Human Mating with Neanderthals and Denisovans Revealed by DNA

Maddie Burakoff and Laura Ungar of Associated Press wrote: DNA has revealed there were other interactions, ones that changed who we are today. In 2010, the Swedish geneticist Svante Paabo and his team pieced a tricky puzzle together. They were able to assemble fragments of ancient DNA into a full Neanderthal genome, a feat that was long thought to be impossible and won Paabo a Nobel Prize in 2022. [Source: Maddie Burakoff and Laura Ungar, Associated Press, September 24, 2023]

This ability to read ancient DNA revolutionized the field, and it is constantly improving. For example, when scientists applied these techniques to a pinky bone and some huge molars found in a Siberian cave, they found genes that didn’t match anything seen before, said Bence Viola, an anthropologist at the University of Toronto who was part of the research team that made the discovery. It was a new species of hominin, now known as Denisovans, who were the first human cousins identified only by their DNA.

Armed with these Neanderthal and Denisovan genomes, scientists could compare them to people today and look for chunks of DNA that match. When they did, they found clear signs of crossover. The DNA evidence showed that Homo sapiens mated with groups including Neanderthals and Denisovans. It even revealed evidence of other “ghost populations” — groups who are part of our genetic code, but whose fossils we haven’t found yet.

It’s hard to pin down exactly when and where these interactions happened. Our ancestors seem to have mixed with the Neanderthals soon after leaving Africa and heading into Europe. They probably bumped into the Denisovans in parts of East and Southeast Asia. “They didn’t have a map, they didn’t know where they were going,” the Smithsonian's Potts said. “But looking over the next hillside into the next valley, (they) ran into populations of people that looked a bit different from themselves, but mated, exchanged genes.” So even though Neanderthals did look distinct from Homo sapiens — from their bigger noses to their shorter limbs — it wasn’t enough to create a “wall” between the groups, Shea said. “They probably thought, ‘Oh, these guys look a little bit different,’” Shea said. “‘Their skin color’s a little different. Their faces look a little different. But they’re cool guys, let’s go try to talk to them.’”

Neanderthal and Denisovan DNA in Humans Today

Laura Ungar and Maddie Burakoff of Associated Press wrote: Research shows some African populations have almost no Neanderthal DNA, while those from European or Asian backgrounds have 1 percent to 2 percent. Denisovan DNA is barely detectable in most parts of the world but makes up 4 percent to 6 percent of the DNA of people in Melanesia, which extends from New Guinea to the Fiji Islands. That may not sound like much, but it adds up: Even though only 100,000 Neanderthals ever lived, “half of the Neanderthal genome is still around, in small pieces scattered around modern humans,” said Zeberg, who collaborates closely with Paabo.[Source: Laura Ungar and Maddie Burakoff, Associated Press, September 25, 2023]

It's also enough to affect us in very real ways. Scientists don’t yet know the full extent, but they’re learning it can be both helpful and harmful. For example, Neanderthal DNA has been linked to auto-immune diseases like Graves’ disease and rheumatoid arthritis. When Homo sapiens came out of Africa, they had no immunity to diseases in Europe and Asia, but Neanderthals and Denisovans already living there did.

“By interbreeding with them, we got a quick fix to our immune systems, which was good news 50,000 years ago,” said Chris Stringer, a human evolution researcher at the Natural History Museum in London. “The result today is, for some people, that our immune systems are oversensitive, and sometimes they turn on themselves.”

Similarly, a gene associated with blood clotting believed to be passed down from Neanderthals in Eurasia may have been helpful in the “rough and tumble world of the Pleistocene,” said Rick Potts, director of the human origins program at the Smithsonian Institution. But today it can raise the risk of stroke for older adults. “For every benefit,” he said, “there are costs in evolution.”

In 2020, research by Zeberg and Paabo found that a major genetic risk factor for severe COVID-19 is inherited from Neanderthals. “We compared it to the Neanderthal genome and it was a perfect match,” Zeberg said. “I kind of fell off my chair.” The next year, they found a set of DNA variants along a single chromosome inherited from Neanderthals had the opposite effect: protecting people from severe COVID. The list goes on: Research has linked Neanderthal genetic variants to skin and hair color, behavioral traits, skull shape and Type 2 diabetes. One study found that people who report feeling more pain than others are likely to carry a Neanderthal pain receptor. Another found that a third of women in Europe inherited a Neanderthal receptor for the hormone progesterone, which is associated with increased fertility and fewer miscarriages.

Much less is known about our genetic legacy from Denisovans — although some research has linked genes from them to fat metabolism and better adaptation to high altitudes. Maanasa Raghavan, a human genetics expert at the University of Chicago, said a stretch of Denisovan DNA has been found in Tibetans, who continue to live and thrive in low-oxygen environments today. Scientists have even found evidence of “ghost populations" — groups whose fossils have yet to be discovered — within modern humans' genetic code.

'Ghost Population' That Mated with Ancestors of Modern Humans in West Africa

Ancestors of people living in present-day West Africa appear to have reproduced with a species of ancient humans unknown to scientists, a study published in February 2020 in the journal Science Advances suggests. Our human ancestors in Europe mated with Neanderthals and ancestor of people in now living Oceania mated with Denisovans, and scientists say the genetic variation within West African populations is different enough that it is best explained by mating with a different, unknown “ghost” human species. [Source: Ryan W. Miller, USA TODAY, February 14, 2020]

“"This continues the story that we've been seeing in studies throughout the past decade: There's lots more interbreeding between lots of human populations than we were aware of ever before," Alan Rodgers, an anthropologist and the lead author of the new study, told Business Insider. "This discovery has pushed the time depth of those interbreedings much farther back." [Source: Aylin Woodward,, Business Insider, February 21, 2020]

The analysis compared DNA from Neanderthals, Denisovans, and modern humans from Europe and Africa. Ryan W. Miller wrote in USA TODAY: “With difficulties in obtaining a full fossil records and ancient DNA, scientists' understanding of the genetic diversity within West African populations has been poor. To get a fuller picture, researchers at University of California, Los Angeles compared 405 genomes of West Africans with Neanderthal and Denisovan genomes.

“Sriram Sankararaman, one of the study's authors, told NPR that the researchers used statistical modeling to figure out which parts of the DNA they were analyzing did not come from modern humans, then compare those to the two ancient hominin species. What they found is the presence of DNA from "an archaic ghost population" in modern West African populations' genetic ancestry. “"We don't have a clear identity for this archaic group," Sankararaman told NPR. "That's why we use the term 'ghost.' It doesn't seem to be particularly closely related to the groups from which we have genome sequences from."

Sankararaman and co-author Arun Durvasula found this introgression, or sharing of genetic information between two species, between the "ghost population" and ancestors of West Africans may have occurred within the last 124,000 years. The "ghost population" likely split from humans and Neanderthals into a new species between 360,000 to 1.02 million years ago, the study says. The study also says the breeding may have occurred over an extended period of time, rather than all at once. “John Hawks, an anthropologist at the University of Wisconsin-Madison, told The Guardian: “This interbreeding may also have a great impact on the genetic makeup of modern populations: Anywhere from 2 percent to 19 percent of their genetic ancestry could be derived from the "ghost population."

'Ghost Population' That Mated with Ancestors of Neanderthals and Denisovans in Eurasia 700,000 Years Ago

According to the study by the team lead by Alan Rodgers, published in February 21, 2020 in the journal Science Advances, ancestors of Neanderthals and Denisovans interbred with a mysterious population of ancient hominins in Eurasia 700,000 years ago. It's the earliest known example of mating between different hominin populations. This ghost population here was a distinct, unknown population that had separated from other hominin species at least 1 million years prior to the mating even [Source: Aylin Woodward,, Business Insider, February 21, 2020]

Aylin Woodward wrote in Business Insider: A major implication of the study, then, is that hominin populations migrated from Africa to Eurasia three times during our long evolutionary history: once 1.9 million years ago, again 700,000 years ago, and then a final time 50,000 years ago. The first of these waves involved the "superarchaics." Then the neandersovans followed 700,000 years ago; they likely separated from the modern human lineage before they migrated north, the study suggests. As that second wave of ancestors moved into Eurasia, the researchers wrote, they likely "interbred with indigenous Eurasians, largely replaced them, and separated into eastern and western subpopulations — Denisovans and Neanderthals."

Then many hundreds of thousands of years later, modern humans left Africa, interbreeding with Neanderthals — and eventually Denisovans, too — as they spread through Eurasia. "These same events unfolded once again around 50,000 years ago as modern humans expanded out of Africa and into Eurasia, largely replacing the Neanderthals and Denisovans," the study authors wrote.

Rodgers' team's discovery came after they compared publicly available modern human DNA with ancient DNA. The analysis revealed at least four watershed moments in which genetic material passed from one human species to another over the last 1 million years. Three of those moments matched the results other studies had already found. But the oldest instance was a new find.In addition to representing the oldest evidence of human interbreeding on record, the finding is also surprising because but the two populations that mated were far less closely related than other human groups previously known to have interbred. Whereas modern humans and Neanderthals had been on separate branches of the evolutionary tree for about 750,000 years when they interbred, the newly discovered population and the "neandersovans" had been separated for more than 1 million years.

“Several mysteries remain, however. Rodgers' team isn't sure what ancient species the "superarchaic" population belonged to. All they know is that genetic evidence suggests the superarchaics separated from our human lineage about 2 million years ago, and that ancient humans were living in Eurasia at the time the species separation occurred. "We've got fossil evidence of humans in Eurasia that dates back to 1.85 million years old," Rogers said.

“At least two groups of human species, or taxa, lived in Eurasia during the time the superarchaics broke off from our lineage. One, Homo erectus, was the first of our ancestors to walk upright. The other possible taxon was Homo erectus' younger cousin, Homo antecessor, which inhabited modern-day Spain. "Any of those taxa might be the superarchaics," Rodgers said. "Or they might be some taxon we don't know about yet." But regardless of which group the superarchaics belonged to, Rodgers said, the new evidence of interbreeding offers a glimpse into an ancient time period that researchers know very little about. "We're just shedding light on an interval on human evolutionary history that was previously completely dark," he said.

Does Human DNA Reveal That Homo Erectus Mated with a Ghost Ancestor One Million Years Ago?

Stephanie Pappas wrote in Live Science: Today's humans carry the genes of an ancient, unknown ancestor, left there by hominin species intermingling perhaps a million years ago. The ancestor may have been Homo erectus, but no one knows for sure — the genome of that extinct species of human has never been sequenced, said Adam Siepel, a computational biologist at Cold Spring Harbor Laboratory and one of the authors of the paper examining the relationships of ancient human ancestors. The research as published August 6, 2022 in the journal PLOS Genetics. [Source: Stephanie Pappas, Live Science, August 30, 2022]

The researchers of the new study used a computational method of comparing the genomes of two Neanderthals, a Denisovan and two modern African individuals. (Africans were chosen because modern people in Africa don't carry Neanderthal genes from the well-known human-Neanderthal interbreeding that occurred in Europe starting 50,000 years ago.) This method allowed the researchers to capture recombination events, in which segments of chromosomes — which are made up of DNA — from one individual get incorporated into the chromosomes of another.

The researchers found that 1 percent of the Denisovan genome hails from the genes of an unknown ancestor, from an interbreeding event that must have happened, roughly, a million years ago. The interbreeding event were passed along again to modern humans: 15 percent of the interbreeding sequences found in Denisovans are present in people living today, the researchers found. This mystery ancestor could have been Homo erectus, Siepel said, because Homo erectus likely did overlap in Eurasia with the ancestors of Denisovans and Neanderthals. However, these fragments are tiny and there are no Homo erectus sequences to compare them to, so this is speculative.

Smart and Artistic Neanderthals

Maddie Burakoff and Laura Ungar of Associated Press wrote: The idea that modern humans, and particularly white humans, were the pinnacle of evolution came from a time of “colonialism and elitism,” said Janet Young, curator of physical anthropology at the Canadian Museum of History. One Neanderthal painting, created to reflect the vision of a eugenics advocate, made its way through decades of textbooks and museum displays. [Source: Maddie Burakoff and Laura Ungar, Associated Press, September 24, 2023]

The new findings have completely upended the idea that earlier, more ape-like creatures started standing up straighter and getting more complex until they reached their peak form in Homo sapiens, Young said. Along with the genetic evidence, other archaeological finds have shown Neanderthals had complex behaviors around hunting, cooking, using tools and even making art.

Why Did Modern Humans Survive While Other Hominins Went Extinct?

Laura Ungar and Maddie Burakoff of Associated Press wrote: In the past, the tale of modern humans’ survival “was always told as some success story, almost like a hero’s story," in which Homo sapiens rose above the rest of the natural world and overcame the “insufficiencies” of their cousins, Potts said. “Well, that simply is just not the correct story.” Neanderthals and Denisovans had already existed for thousands of years by the time Homo sapiens left Africa. Scientists used to think we won out because we had more complex behavior and superior technology. But recent research shows that Neanderthals talked, cooked with fire, made art objects, had sophisticated tools and hunting behavior, and even wore makeup and jewelry. [Source: Laura Ungar and Maddie Burakoff, Associated Press, September 25, 2023]

Several theories now tie our survival to our ability to travel far and wide. “We spread all over the world, much more than these other forms did,” Zeberg said. While Neanderthals were specially adapted to cold climates, Potts said, Homo sapiens were able to disperse to all different kinds of climates after emerging in tropical Africa. “We are so adaptable, culturally adaptable, to so many places in the world,” he said. Meanwhile, Neanderthals and Denisovans faced harsh conditions in the north, like repeated ice ages and ice sheets that likely trapped them in small areas, said Eleanor Scerri, an archeologist at Germany’s Max Planck Institute for Geoanthropology. They lived in smaller populations with a greater risk of genetic collapse.

Plus, we had nimble, efficient bodies, Prendergast said. It takes a lot more calories to feed stocky Neanderthals than comparatively skinny Homo sapiens, so Neanderthals had more trouble getting by, and moving around, especially when food got scarce. Janet Young, curator of physical anthropology at the Canadian Museum of History, pointed to another intriguing hypothesis — which anthropologist Pat Shipman shared in one of her books –- that dogs played a big part in our survival. Researchers found the skulls of domesticated dogs in Homo sapiens sites much further back in time than anyone had found before. Scientists believe dogs made hunting easier. By around 30,000 years ago, all the other kinds of hominins on Earth had died off, leaving Homo sapiens as the last humans standing.

Image Sources: Wikimedia Commons

Text Sources: Live Science, Nature, National Geographic, New York Times, Washington Post, Los Angeles Times, Smithsonian magazine, Nature, Scientific American. Discover magazine, Discovery News, Natural History magazine, Archaeology magazine, The New Yorker, Time, BBC, The Guardian, Reuters, AP, AFP and various books and other publications.

Last updated May 2024